This function calculates the degree to which a subset of genes (i.e.
a "signature") is biased in the ordered list of all genes. The
function is typically used internally by dksClassify,
but the user may want to call it directly to inspect the running
sums.
Usage
KS(data, geneset, decreasing=TRUE, method="kort")
Arguments
data
A vector of gene expression data. The data need not
be sorted, as the function will sort it itself.
geneset
A DKSGeneSet object, such as one of
the slots of the DKSClassifier returned by
link{dksClassify}.
decreasing
Indicates which way data should be sorted.
If TRUE, the degree of upregulation will be scored. If FALSE,
the degree of down regulation will be scored.
method
Two methods are supported. The 'kort' method returns
the maximum of the running sum. The 'yang' method
returns the sum of the maximum and the minimum of the
running sum, thereby penalizing classes that are highly enriched
in a subset of genes of a given signature, but highly
down regulated in another subset of that same signature.
Value
runningSums
A matrix with 1 row per gene and 1 column per
signature. The value is the running sum of the KS metric
at each point along the sorted list of genes. The maximum
of this column vector corresponds to the KS score for the
corresponding signature.
ksScores
A named vector giving the KS score for each signature.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(dualKS)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: affy
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/dualKS/KS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: KS
> ### Title: Calculate Kolmogorov Smirnov rank sum scores.
> ### Aliases: KS
> ### Keywords: classif
>
> ### ** Examples
>
>
> data("dks")
> tr <- dksTrain(eset, 1, "both")
> cl <- dksSelectGenes(tr, 100)
> sc <- KS(exprs(eset)[,1], cl@genes.up)
> plot(sc$runningSums[,1], type='l')
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.